Michael,
If it is a club team that you are speaking about and not a team governed under the school's athletic dept., I don't think the NCAA would care at all. The team would not be considered varsity and would not impact the "official" school teams.

I do not think there is anything stopping (besides funds!) a school's club sports and recreation dept from offering scholarships for a club sport.
Now, I could see that an athletic dept. would object to any duplicate sports (varsity baseball AND club baseball) with scholarships.